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Although leishmaniasis has been reported in the indigenous Taiwanese population, the last sand fly survey, based on morphological features, was conducted over two decades ago. Thus, updated information on the phlebotomine sand fly fauna and disease transmission risk in Taiwan is required. In this study, a nationwide survey was conducted using molecular methods to ascertain the current sand fly status and disease transmission risk in Taiwan.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>A total of 1292 sand flies were collected in a nationwide survey conducted in 2017\u20132018. Species were identified based on their 18S ribosomal DNA (<jats:italic>18S rDNA<\/jats:italic>), cytochrome c oxidase subunit I (<jats:italic>COI<\/jats:italic>), and cytochrome b (<jats:italic>Cytb<\/jats:italic>) using the phylogenetic tree and intra- and interspecific divergence analysis. The relative abundance, richness, diversity, and evenness of sand fly species were also calculated.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Phylogenetic analysis showed six independent clades, including <jats:italic>Phlebotomus kiangsuensis<\/jats:italic> (0.1%), <jats:italic>Sergentomyia iyengari<\/jats:italic> (93.7%), <jats:italic>Sergentomyia barraudi<\/jats:italic> (3.8%), <jats:italic>Sergentomyia squamipleuris<\/jats:italic> (1.6%), and two species described for the first time (0.9%). Species divergence analysis supported the phylogenetic results. The richness and abundance of sand flies were higher in eastern Taiwan than in western regions. Blood-source analysis showed an interaction between <jats:italic>Se. iyengari<\/jats:italic> and humans. In addition, no <jats:italic>Leishmania<\/jats:italic> spp. DNA was detected in any specimen, which suggests a low transmission risk for <jats:italic>Leishmania<\/jats:italic> spp. in Taiwan.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>These findings provide valuable knowledge on the current fauna of phlebotomine sand flies, which is beneficial for assessing disease risk and managing vector control in Taiwan.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Graphical abstract<\/jats:title>\n          <\/jats:sec>","DOI":"10.1186\/s13071-025-07017-1","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T13:00:39Z","timestamp":1760014839000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A morphological and molecular study of phlebotomine sand flies of Taiwan reveals the record of six species"],"prefix":"10.1186","volume":"18","author":[{"given":"Han-Hsuan","family":"Chung","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng-Hui","family":"Tsai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hwa-Jen","family":"Teng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiu\u2010Ling","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"7017_CR1","doi-asserted-by":"crossref","unstructured":"Service M. 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